How to run husky pre-commit in child directory only

I faced the same issue. I fixed it by installing husky in the main directory.
my setup:

/project
    .git
    package.json
    /frontend
        package.json
    /frontend-admin
        package.json

In /project/package.json:

{
  "license": "MIT",
  "version": "0.0.1",
  "private": true,
  "scripts": {
    "frontend": "cd frontend && yarn lint"
    "frontend:admin": "cd frontend-admin && yarn lint",
  },
  "husky": {
    "hooks": {
      "pre-commit": "npm-run-all frontend frontend:admin"
    }
  },
  // In the main folder you should install husky 
  // and npm-run-all to execute multiple commands
  "dependencies": {
    "husky": "^4.3.0",
    "npm-run-all": "^4.1.5"
  }
}

Your subdirectory should have a lint script to execute.
When one of the scripts crashes husky will give a report and abort immediately.

While this question is a few years old. Hopefully someone will benefit from an updated answer provided by the folks from husky.

TL;DR

See the new guidance here.

For those that w@ntz answ3rz n0wz!!

New guidance that is provided in the typicode/husky-init README.md suggests the following when "your package.json file and .git directory are not at the same level. For example, project/.git and project/front/package.json"

You can change directory during prepare script and pass a subdirectory:

// package.json
{
  "scripts": {
    "prepare": "cd .. && husky install front/.husky"
  }
}

Is it possible to only have the hooks run if you are IN a certain folder when you commit?

No, but the hook itself can determine which directory it was in when it was run. This is not properly documented, but GIT_PREFIX is set in the environment before Git chdir-s to the $GIT_WORK_TREE or $GIT_DIR directory. (This has been the case since Git version 1.7.8.)